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- PDB-2f9h: The Crystal Structure of PTS System IIA Component from Enterococc... -

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Basic information

Entry
Database: PDB / ID: 2f9h
TitleThe Crystal Structure of PTS System IIA Component from Enterococcus faecalis V583
ComponentsPTS system, IIA component
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta structure / beta-barrel / dimer / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


protein-N(PI)-phosphohistidine-sugar phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / cytoplasm
Similarity search - Function
Phosphotransferase system, glucitol/sorbitol-specific IIA component / Phosphotransferase system, glucitol/sorbitol-specific IIA component / Phosphotransferase system, glucitol/sorbitol-specific IIA component superfamily / PTS system glucitol/sorbitol-specific IIA component / PTS_EIIA type-5 domain profile. / M1 Pyruvate Kinase; Domain 3 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
: / PTS system, IIA component
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.57 Å
AuthorsKim, Y. / Quartey, P. / Moy, S. / Bargassa, M. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published / Year: 2006
Title: The Crystal Structure of PTS System IIA Component from Enterococcus faecalis V583
Authors: Kim, Y. / Quartey, P. / Abdullah, J. / Collart, F. / Joachimiak, A.
History
DepositionDec 5, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PTS system, IIA component
B: PTS system, IIA component


Theoretical massNumber of molelcules
Total (without water)28,3712
Polymers28,3712
Non-polymers00
Water4,630257
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-13 kcal/mol
Surface area10640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.249, 58.249, 140.443
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein PTS system, IIA component


Mass: 14185.389 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: GenBank: 29377088, UniProt: Q831B0*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M Sodium acetate pH 4.6, 4% PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-BM10.9793, 0.9795
SYNCHROTRONAPS 19-ID20.9793
Detector
TypeIDDetectorDateDetails
SBC-31CCDJul 25, 2005mirrors
ADSC QUANTUM 3152CCDNov 22, 2005mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystal monochromator, Si(111)MADMx-ray1
2double crystal monochromator, Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97951
ReflectionResolution: 1.57→34.32 Å / Num. all: 39333 / Num. obs: 38988 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.7 % / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 17.3
Reflection shellResolution: 1.57→1.63 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 4.5 / Num. unique all: 3411 / % possible all: 88.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
MLPHAREphasing
RESOLVEphasing
SHELXEmodel building
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.57→34.32 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1411320.03 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Crystal was twinned; fraction 0.442, direction -h,-k,l
RfactorNum. reflection% reflectionSelection details
Rfree0.229 3615 9.3 %RANDOM
Rwork0.169 ---
all0.174 38693 --
obs0.169 38693 98.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.0654 Å2 / ksol: 0.348908 e/Å3
Displacement parametersBiso mean: 25.4 Å2
Baniso -1Baniso -2Baniso -3
1-2.29 Å20.6 Å20 Å2
2--2.29 Å20 Å2
3----4.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 1.57→34.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1844 0 0 257 2101
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.451.5
X-RAY DIFFRACTIONc_mcangle_it2.332
X-RAY DIFFRACTIONc_scbond_it2.632
X-RAY DIFFRACTIONc_scangle_it3.912.5
LS refinement shellResolution: 1.57→1.64 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2979 403 8.78 %
Rwork0.2819 3540 -
obs-5217 85.86 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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